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- PDB-2evu: Crystal structure of aquaporin AqpM at 2.3A resolution -

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Basic information

Entry
Database: PDB / ID: 2evu
TitleCrystal structure of aquaporin AqpM at 2.3A resolution
ComponentsAquaporin aqpM
KeywordsMEMBRANE PROTEIN / alpha-helical / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP
Function / homology
Function and homology information


channel activity / plasma membrane
Similarity search - Function
Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Aquaporin transporter / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMethanothermobacter marburgensis str. Marburg (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLee, J.K. / Kozono, D. / Remis, J. / Kitagawa, Y. / Agre, P. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 A.
Authors: Lee, J.K. / Kozono, D. / Remis, J. / Kitagawa, Y. / Agre, P. / Stroud, R.M.
History
DepositionOct 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aquaporin aqpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4949
Polymers25,3571
Non-polymers1,1378
Water2,198122
1
A: Aquaporin aqpM
hetero molecules

A: Aquaporin aqpM
hetero molecules

A: Aquaporin aqpM
hetero molecules

A: Aquaporin aqpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,97636
Polymers101,4274
Non-polymers4,54932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area22080 Å2
ΔGint-168 kcal/mol
Surface area29690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.887, 93.887, 77.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Aquaporin aqpM


Mass: 25356.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter marburgensis str. Marburg (archaea)
Species: Methanothermobacter marburgensis / Strain: Marburg / DSM 2133 / Gene: aqpM / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(DE3)RIL / References: UniProt: Q9C4Z5
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% PEG 4000, 50 mM TRIS pH 9, 100 mM NaCl, 10% glycerol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 16104 / Num. obs: 15208 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.37 Å / % possible all: 86

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.226 1512 random
Rwork0.188 --
all0.188 16104 -
obs0.188 15208 -
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 76 122 1978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.3→2.44 Å
RfactorNum. reflection% reflection
Rfree0.275 197 -
Rwork0.322 --
obs-1947 86 %

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